Foundation for Neglected Disease Research

Antimicrobial resistance is a global health threat that requires the development of new treatment concepts. These should not only overcome existing resistance but be designed to slow down the emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We are extending this concept by developing proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs are derived from cyclomarins which, when dimerized, generate compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduce levels of endogenous ClpC1 in Mycobacterium smegmatis and display minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug-resistant Mtb isolates. The compounds also kill Mtb residing in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.

Antimicrobial resistance is a global health threat that requires development of new treatment concepts. These should not only overcome existing resistance, but be designed to slow down emergence of new resistance mechanisms. Targeted protein degradation, whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. We developed proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mycobacterium tuberculosis (Mtb) BacPROTACs were derived from cyclomarins, natural products known to bind to ClpC1, which were dimerized resulting in compounds that recruit and degrade ClpC1. The resulting Homo-BacPROTACs reduced levels of endogenous ClpC1 in Mycobacterium smegmatis, as well as displayed minimum inhibitory concentrations in the low micro- to nanomolar range in mycobacterial strains, including multiple drug resistant Mtb isolates. The compounds also killed Mtb resident in macrophages. Thus, Homo-BacPROTACs that degrade ClpC1 represent a different strategy for targeting Mtb and overcoming drug resistance.

Has the COVID-19 pandemic nudged the scientific establishment and biotech ecosystem in India to focus on social impact and translational biology in the human health space? We address this first by reexamining the promise of science to society, namely, can and should the pursuit of knowledge be harnessed for the improvement of human life (utility)? We emphasize the possibility of pursuits that both expand the frontiers of the known and are useful, namely the “Pasteur’s quadrant.” Overlay this position with the conditions that support recombinant growth, which is the ability to combine existing knowledge into forms and products that are more valuable or in synchrony with what is needed, and you are likely to zoom in on where India is today. We use anecdotes and vignettes of how scientists, scientific institutions, and the biotechnology industry responded to the COVID-19 pandemic to illustrate the fertility of the Pasteur’s quadrant, supplemented with inklings of recombinant growth. Based on these data, we offer an optimistic view that Indian science and industry are poised to find the sweet spot in the landscape of knowledge and usefulness — such that both human creativity and human societies can flourish. Such developments are likely to stand us in good stead, particularly as we rise to the challenge of emerging diseases and antibiotic resistance.

Mycobacterial pathogens, including nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis, are pathogens of significant worldwide interest owing to their inherent drug resistance to a wide variety of FDA-approved drugs as well as causing a broad range of serious infections. Identifying new antibiotics active against mycobacterial pathogens is an urgent unmet need, especially those antibiotics that can bypass existing resistance mechanisms. In this study, we demonstrate that gepotidacin, a first-in-class triazaacenapthylene topoisomerase inhibitor, demonstrates potent activity against M. tuberculosis and M. fortuitum, as well as against other clinically relevant NTM species, including fluoroquinolone-resistant M. abscessus. Furthermore, gepotidacin exhibits concentration-dependent bactericidal activity against various mycobacterial pathogens, synergizes with several drugs utilized for their treatment, and reduces bacterial load in macrophages in intracellular killing assays comparably to amikacin. Additionally, M. fortuitum ATCC 6841 was unable to generate resistance to gepotidacin in vitro. When tested in a murine neutropenic M. fortuitum infection model, gepotidacin caused a significant reduction in bacterial load in various organs at a 10-fold lower concentration than amikacin. Taken together, these findings show that gepotidacin possesses a potentially new mechanism of action that enables it to escape existing resistance mechanisms. Thus, it can be projected as a potent novel lead for the treatment of mycobacterial infections, particularly for NTM, where present therapeutic interventions are extremely limited.

Antimicrobial resistance (AMR) is a global public health threat that urgently requires development of new treatment concepts. In general, these treatments should not only be able to overcome existing resistance, but designed to slow down or prevent emergence of new resistance mechanisms. Targeted protein degradation (TPD), whereby a drug redirects cellular proteolytic machinery towards degrading a specific target, is an emerging concept in drug discovery. Here, we demonstrate that a TPD strategy represents an effective approach for addressing AMR in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB) and one of the deadliest bacterial pathogens. We developed proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery. The anti-Mtb BacPROTACs were derived from cyclomarins, natural products known to bind to ClpC1. To create dual targeting modalities, cyclomarins were dimerized by click chemistry or olefin metathesis, resulting in compounds that recruit and degrade ClpC1. The resulting BacPROTACs reduced levels of endogenous ClpC1 in a model organism Mycobacterium smegmatis (Msm), as well as displayed minimum inhibitory concentrations in the low micro- to nanomolar range in Msm and Mtb strains, including multiple drug resistant isolates. Additionally, the compounds also killed Mtb resident in macrophages. Taken together, anti-Mtb BacPROTACs that degrade ClpC1, a core component of the mycobacterial protein degradation machinery, represent a fundamentally different strategy for targeting Mtb and overcoming drug resistance.

The capacity of Mycobacterium tuberculosis (Mtb) to tolerate multiple antibiotics represents a major problem in tuberculosis (TB) management. Heterogeneity in Mtb populations is one of the factors that drives antibiotic tolerance during infection. However, the mechanisms underpinning this variation in bacterial population remain poorly understood. Here, we show that phagosomal acidification alters the redox physiology of Mtb to generate a population of replicating bacteria that display drug tolerance during infection. RNA sequencing of this redox-altered population revealed the involvement of iron-sulfur (Fe-S) cluster biogenesis, hydrogen sulfide (H2S) gas, and drug efflux pumps in antibiotic tolerance. The fraction of the pH- and redox-dependent tolerant population increased when Mtb infected macrophages with actively replicating HIV-1, suggesting that redox heterogeneity could contribute to high rates of TB therapy failure during HIV-TB coinfection. Pharmacological inhibition of phagosomal acidification by the antimalarial drug chloroquine (CQ) eradicated drug-tolerant Mtb, ameliorated lung pathology, and reduced postchemotherapeutic relapse in in vivo models. The pharmacological profile of CQ (C max and AUClast) exhibited no major drug-drug interaction when coadministered with first line anti-TB drugs in mice. Our data establish a link between phagosomal pH, redox metabolism, and drug tolerance in replicating Mtb and suggest repositioning of CQ to shorten TB therapy and achieve a relapse-free cure.

A set of 12 novel hydroxamate compounds (NHCs), structurally designed as inhibitors of histone deacetylase (HDAC) enzyme, were synthesized at our facility. These were adamantane derivatives with N-hydroxyacetamide as pharmacophore, and each of these compounds was tested for potentiating activity on fluconazole. The concentration of fluconazole which completely inhibited (concentration of complete inhibition [CCI]) the growth of Candida albicans ATCC 90028 and C. albicans ATCC 64550 was determined by micro-dilution method in the absence and presence of NHCs. The CCI of fluconazole without the NHC combination was 64 μg/ml and 1024 μg/ml against C. albicans ATCC 90028 and C. albicans ATCC 64550, respectively. The majority of the NHCs potentiated the fluconazole activity markedly as CCI of fluconazole against C. albicans ATCC 90028 reduced to 0.25 μg/ml. Similarly, CCI of fluconazole against C. albicans ATCC 64550 reduced to 4–8 μg/ml in combination with majority of NHCs while the best activity was displayed by the compound 1 with a reduction of CCI to 0.5 μg/ml. The study results revealed the potential usage of hydroxamate derivatives, structurally designed as HDAC inhibitors to enhance the activity of fluconazole against C. albicans.